[2024-01-24 12:40:50,505] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:50,508] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:50,509] [INFO] DQC Reference Directory: /var/lib/cwl/stgdb7beb58-3f63-4289-b3f5-f77199def592/dqc_reference
[2024-01-24 12:40:51,780] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:51,781] [INFO] Task started: Prodigal
[2024-01-24 12:40:51,781] [INFO] Running command: gunzip -c /var/lib/cwl/stgc475b978-fc66-4c70-bc72-df43b4ea155f/GCF_000170955.2_ASM17095v2_genomic.fna.gz | prodigal -d GCF_000170955.2_ASM17095v2_genomic.fna/cds.fna -a GCF_000170955.2_ASM17095v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:53,863] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:53,864] [INFO] Task started: HMMsearch
[2024-01-24 12:40:53,864] [INFO] Running command: hmmsearch --tblout GCF_000170955.2_ASM17095v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdb7beb58-3f63-4289-b3f5-f77199def592/dqc_reference/reference_markers.hmm GCF_000170955.2_ASM17095v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:54,098] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:54,099] [INFO] Found 6/6 markers.
[2024-01-24 12:40:54,119] [INFO] Query marker FASTA was written to GCF_000170955.2_ASM17095v2_genomic.fna/markers.fasta
[2024-01-24 12:40:54,120] [INFO] Task started: Blastn
[2024-01-24 12:40:54,120] [INFO] Running command: blastn -query GCF_000170955.2_ASM17095v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb7beb58-3f63-4289-b3f5-f77199def592/dqc_reference/reference_markers.fasta -out GCF_000170955.2_ASM17095v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:54,729] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:54,733] [INFO] Selected 10 target genomes.
[2024-01-24 12:40:54,734] [INFO] Target genome list was writen to GCF_000170955.2_ASM17095v2_genomic.fna/target_genomes.txt
[2024-01-24 12:40:54,737] [INFO] Task started: fastANI
[2024-01-24 12:40:54,737] [INFO] Running command: fastANI --query /var/lib/cwl/stgc475b978-fc66-4c70-bc72-df43b4ea155f/GCF_000170955.2_ASM17095v2_genomic.fna.gz --refList GCF_000170955.2_ASM17095v2_genomic.fna/target_genomes.txt --output GCF_000170955.2_ASM17095v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:58,050] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:58,051] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdb7beb58-3f63-4289-b3f5-f77199def592/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:58,051] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdb7beb58-3f63-4289-b3f5-f77199def592/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:58,063] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:40:58,064] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:40:58,064] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Borreliella valaisiana	strain=VS116	GCA_000170955.2	62088	62088	type	True	100.0	413	413	95	conclusive
Borreliella yangtzensis	strain=DSM 24625	GCA_014201775.1	683292	683292	type	True	94.3807	359	413	95	below_threshold
Borreliella garinii	strain=CIP 103362	GCA_001922545.1	29519	29519	type	True	91.9807	354	413	95	below_threshold
Borreliella garinii	strain=20047	GCA_003814405.1	29519	29519	type	True	91.8472	364	413	95	below_threshold
Borreliella afzelii	strain=DSM 10508	GCA_014202295.1	29518	29518	type	True	91.5676	360	413	95	below_threshold
Borreliella japonica	strain=ATCC 51557	GCA_900099615.1	34095	34095	type	True	91.375	354	413	95	below_threshold
Borreliella lanei	strain=DSM 17992	GCA_014205895.1	373540	373540	type	True	91.2075	347	413	95	below_threshold
Borreliella mayonii	strain=MN14-1420	GCA_001945665.1	1674146	1674146	type	True	91.0021	370	413	95	below_threshold
Borreliella burgdorferi	strain=FDAARGOS_196	GCA_002083055.2	139	139	type	True	90.7431	367	413	95	below_threshold
Borreliella bissettiae	strain=DN127	GCA_000222305.1	64897	64897	type	True	90.5517	360	413	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:58,066] [INFO] DFAST Taxonomy check result was written to GCF_000170955.2_ASM17095v2_genomic.fna/tc_result.tsv
[2024-01-24 12:40:58,066] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:58,066] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:58,067] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdb7beb58-3f63-4289-b3f5-f77199def592/dqc_reference/checkm_data
[2024-01-24 12:40:58,067] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:58,087] [INFO] Task started: CheckM
[2024-01-24 12:40:58,087] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000170955.2_ASM17095v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000170955.2_ASM17095v2_genomic.fna/checkm_input GCF_000170955.2_ASM17095v2_genomic.fna/checkm_result
[2024-01-24 12:41:12,445] [INFO] Task succeeded: CheckM
[2024-01-24 12:41:12,447] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:41:12,468] [INFO] ===== Completeness check finished =====
[2024-01-24 12:41:12,469] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:41:12,469] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000170955.2_ASM17095v2_genomic.fna/markers.fasta)
[2024-01-24 12:41:12,470] [INFO] Task started: Blastn
[2024-01-24 12:41:12,470] [INFO] Running command: blastn -query GCF_000170955.2_ASM17095v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb7beb58-3f63-4289-b3f5-f77199def592/dqc_reference/reference_markers_gtdb.fasta -out GCF_000170955.2_ASM17095v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:13,414] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:13,419] [INFO] Selected 9 target genomes.
[2024-01-24 12:41:13,420] [INFO] Target genome list was writen to GCF_000170955.2_ASM17095v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:41:13,424] [INFO] Task started: fastANI
[2024-01-24 12:41:13,425] [INFO] Running command: fastANI --query /var/lib/cwl/stgc475b978-fc66-4c70-bc72-df43b4ea155f/GCF_000170955.2_ASM17095v2_genomic.fna.gz --refList GCF_000170955.2_ASM17095v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000170955.2_ASM17095v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:16,380] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:16,394] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:41:16,395] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_000170955.2	s__Borreliella valaisiana	100.0	413	413	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borreliella	95.0	99.52	99.04	0.95	0.92	14	conclusive
GCF_014201775.1	s__Borreliella yangtzensis	94.276	361	413	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borreliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001922545.1	s__Borreliella garinii	91.977	354	413	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borreliella	95.0	97.97	96.83	0.94	0.85	112	-
GCF_014202295.1	s__Borreliella afzelii	91.5424	360	413	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borreliella	95.0	99.29	99.08	0.96	0.92	10	-
GCF_900099615.1	s__Borreliella japonica	91.375	354	413	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borreliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008828755.2	s__Borreliella turdi	91.3062	353	413	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borreliella	95.0	99.10	99.04	0.96	0.96	3	-
GCF_014205895.1	s__Borreliella lanei	91.2075	347	413	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borreliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001945665.1	s__Borreliella mayonii	90.9974	370	413	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borreliella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000008685.2	s__Borreliella burgdorferi	90.6767	376	413	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borreliella	96.6606	99.04	98.60	0.96	0.83	102	-
--------------------------------------------------------------------------------
[2024-01-24 12:41:16,396] [INFO] GTDB search result was written to GCF_000170955.2_ASM17095v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:16,397] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:16,401] [INFO] DFAST_QC result json was written to GCF_000170955.2_ASM17095v2_genomic.fna/dqc_result.json
[2024-01-24 12:41:16,401] [INFO] DFAST_QC completed!
[2024-01-24 12:41:16,402] [INFO] Total running time: 0h0m26s